The Shadows of the Past
by Tailic
Summary: Baised on the game Shadow the Hedgehog. Shadow is on a quest to find his lost past and ends up caught in the middle of a war against the Black Arms. Is Shadow gonna help Sonic and friends, or will Black Doom suscessfully turn Shadow to his side?
1. Who is Shadow the Hedgehog?

_Pre-Chapter Notes_

OK, before I start the story, you may need to know what it's about. Well, if you played the game, "Shadow the Hedgehog" you'll already know since this fan-fic is a "Losely" based on it. You will later understand what I mean by "Losely". This fan-fic I finally had the courage to post for the public to read, I'm actually trying to convert this into comic form (of course, it's coming along very slowly.) So, on to the story!

Shadow the Hedgehog, Sonic the Hedgehog, and all other characters are copyright to SEGA and Sonic Team.

_**The Shadows of the Past**_

_Prologue: Who is Shadow the Hedgehog?_

"Who am I? What is my reason for being here? What is the purpose for my existence? These questions have haunted me for the past months. But why...why can't I find any answers?" Shadow was thinking this to himself Friday night outside Westopolis City. Shadow was sitting underneath a park lamp, writing in a journal at this time. Beside him was a recent newspaper, only came out yesterday. The headline read "50 Year Return of the Black Comet. Festival Sunday night!"

"The only thing I remember is my name, Shadow the Hedgehog, and..." Shadow then turned to the first page of his journal, which has a drawing of a pretty, but young, girl. "And her, what does she have to do with my past. Any why can't I get that awful image out of head?" This image Shadow was referring to was a flashback, a horrible memory that he can't stop thinking about. The memory had to do with the young girl he drew in his journal, she was running from some soldiers who were chasing her, but in the end, one of the soldiers shot and killed the girl, at that same moment a voice called out "Maria!"

"Why can't I remember anything about my past? Who is this Maria and what does she have to do with anything?" Shadow then picked up the newspaper beside him. "And the Black Comet, I have a feeling that the answers lie with this comet." As soon as Shadow spoke these words, the wind picked up. Dark red clouds covered the once peaceful nighttime sky, and it started to thunder. There was no rain, but there was thunder and lightning. The strong wind took Shadow by surprise and it blew away his journal and newspaper. "Noooo!" Shadow yelled as his stuff blew away into the dark red sky. Anger overcame Shadow. He was angry that he has no answers to his past, angry that he lost his only clues, and angry at Eggman, the only one who he knows has his answers and the one who claims he has no past. In his anger, Shadow somehow caused the light behind him to blow up. He was startled by this sudden small explosion and he didn't notice the black star-like alien behind him until he heard his name being called.

Shadow looked behind him and seen the star-shaped alien project a hologram of a larger black alien with red markings, the alien wore dark-colored robes that just seemed to float in mid-air. Hanging from his robes were large, heavy chains that had Sun and Moon emblems on it in areas. "Shadow, the day has come at last. Find those seven Chaos Emeralds and bring them to me like you said you would." The Black Alien told Shadow in a dark and somewhat raspy voice. Shadow was puzzled, How did this alien know him and does he have the answers to his past? "Wait a Minute! Just who are you and how do you know me? And I've never sais tha..." Shadow was cut off in min-sentence when the hologram disappeared and a couple of laser beams blasted the ground about a couple of feet away from Shadow.

After the Debris settles, Shadow was confused about what all happened. "Whoever that was, I don't know. But since he know who I am, he might hold my answers. If I get a chance to confront him one more time, then I may find my lost past." Shadow then started towards Westopolis in order to confront those aliens and find his answers.


	2. Friends and Foes

**The Shadows of the Past**

_Chapter 1: Friends and Foes_

Westopolis, normally a bustling city filled with cars and people, was now different. Buildings were ruined and crumples, cars were turned over and badly damaged. There were piles of pure rubble were a skyscraper once stood. Laser blasts rained down from the sky and destroyed anything and everything in it's path. The entire city was on fire and all this destruction was caused by these black aliens. GUN tried to stop these aliens, Tried, but many ultimately failed.

Shadow seen all the destruction going on and wondered, should he trust the aliens or should he fight them? But then he told himself that that's a though best revisited later. As Shadow walked along the wreaked street, he noticed a pistol on the ground with about 10 rounds left in it. He picked it up to use it for later in case he needed to defend himself. Shadow didn't have to go far until he seen Sonic battling a couple of flying, bird-like black aliens.

"Hey Shadow, where ya' been? These black creatures are everywhere. Can you help me take them out"Sonic asked Shadow as soon as he spotted him. Sonic didn't notice the bird alien behind him that was about to attack, but Shadow was prepared. Shadow readied his pistol and fired two steady shots at the creature. The creature then disappeared in an explosion of green goop. Sonic turned around just as it happed and then showed a smile of excitement. A sensation of thrill flickered in his emerald green eyes. Sonic then readied a spin dash and rammed into two ground-based aliens. While they were stunned, Shadow fired a coupled of shots at the aliens to get rid of them.

Sonic and Shadow were both doing pretty well fighting off wave after wave of black aliens. Sonic used his traditional methods such as his homing attack and spin dash. Shadow, on the other hand, was using his pistol to fend off the creatures, reloading it with rounds from nearby fallen GUN soldiers.

Watching the battle from overhead was a one-eyed, star-like red and black alien. But another voice seemed to speak through it much like it was a communication device (except it was living, not mechanical) "Hmm, it seems like Shadow has mistaken us as his enemy. No matter, I can easily manipulate him to join my cause. MUWAHAHAHA!" the creature said before flying...errr...floating down to where Shadow was.

The waves of black aliens seemed endless, but Sonic and Shadow were not giving up. The two fearless hedgehogs continued to fend of wave after wave after wave. But they were both starting to get weary from all the fighting. Especially Sonic because he was only using his speed to attack and refused to use any weapon to aid him. Shadow, though, seemed to have the easiest time since the aliens weren't well protected. Only two well placed shots were needed to bring one down. After about 15 more waves of enemies, there was a break in the action. Then the star-like black alien confronted Shadow.

"Why are you helping them?" The Black creature asked Shadow, "They are powerless to stop us. Why don't you join us, that is what you were destined to do." Shadow was confused, how did this...creature know his fate? "The reason I oppose you is because you want the Chaos Emeralds. I will not let anyone take them from their sacred resting place." Shadow said as he threatened the creature with his pistol. Sonic was kinda surprised at what Shadow said "He's starting to sound like Knuckles now" Sonic said to himself with a small laugh, but he needed to tell Shadow the truth. "Umm, Shadow..." Sonic then said while tapping Shadow on the shoulder. "What is it Sonic!" Shadow yelled as he lowered his pistol and turned around to face Sonic. "Umm, the Chaos Emeralds are not on Angel Island anymore."

"WHAT!"

"Those black creatures, we seen them on Angel Island the other night. Me and Tails flew there on the Tornado to see what happened, but we...we were too late. Those black creatures knocked Knuckles out when we got there and they tried to take the emeralds. I did grab the emeralds before they got their grubby hands on them"

"Well, where are the emeralds now and what about the Master Emerald?" Shadow asked after hearing part of Sonic's story. "Before I explain that, I think we should get rid of our visitor first." Sonic said while pointing to the star-like creature behind Shadow. Shadow swiftly turned around and shot the creature several times, knowing that would kill it. "Ok Sonic, tell me everything." Shadow demanded as he turned around to face Sonic. Sonic then proceeded to finish what he said earlier.

"So, you say that the Chaos Emeralds are scattered about again?" Shadow asked after Sonic finished. "Yes, but I know where 3 of them are, we can easily prevent those creatures from getting those ones" Sonic answered. "Where are they!" Shadow demanded as he shook Sonic.

"One is around here in one of the banks, the creatures are still here so they probably didn't find it yet. One is with Tails, he's using it to power the P-3A Tornado. GUN also has one locked away in one of their bases in order to protect it from the creatures"

"And the Master Emerald, where is that?

"Those Black Creatures took it away in one of their gunships"

Suddenly, there was a huge explosion behind Sonic and Shadow. They turned around and seen several black creatures coming out of a hole blasted in the side of a building. That building was...a bank. And one of the creatures that came out was holding a Chaos Emerald. The emerald instantly caught Shadow's eye. "What did you say about them not having it yet?" Shadow said with a smirk before racing off to the creature with the emerald. He then tackled the creature with all his might and speed, then he proceeded to take the emerald, but as soon as his hand touched the emerald, he was engulfed in a bright light emitting from the emerald.

After the light disappeared, Shadow looked around, confused of what happened. He was standing up with the green Chaos Emerald in hand, and all around him were the destroyed and lifeless bodies of the black aliens. Shadow looked at the carnage around him and wondered if it had anything to do with the emerald. "Wow, that was one sweet move, Shadow" Sonic said as he ran up to him "Yeah, but...how did I do it? Unless...: Shadow said as he looked at the Chaos Emerald in his hand. But at that moment, a black alien gunship zoomed past him and snatched his Chaos Emerald.

"Those disgusting Black Creatures, just who do they think they are?" Shadow yelled "I better not let them get the emeralds, though, they might help me find more about my past" Shadow them sped off in pursuit of the alien gunship. "Alright! I don't wanna miss this party for the world!" Sonic then said to himself before showing a brief smile of excitement and then ran off after Shadow.

Yet, back someways in Westopolis, the Star-shaped Black Alien that Shadow shot was still there. There were multiple area where the bullets penetrated his outer scaley skin and a couple of the tentacles were sliced off. But there were no wounds present in the eye. The eye of the creature opened and all the gunshot wounds closed up. Also all of the missing tentacles regrew back again. "Hmhmhmhm. Those fools don't know who they're dealing with. As long as I'm around, my traveling eye is invincible. And soon...soon this puny planet will be no more and Shadow...will work for me. No one can stop the Black Arms!" the creature said before floating off in the direction that Sonic and Shadow went.

Meanwhile at the GUN base right outside westopolis, an officer came bursting in and gave a salute. "Sir, urgent news, sir!" He was speaking to the commander, who turned around and game him a salute. "At ease, officer." The Commander looked to be about in his late 50's. he had grey hair and one blue eye and one orange-ish color eye. "Tell me, what is the urgent news?" he then aksed. The officer then told him.

"Sir, the aliens in Westopolis have been pushed back for now, but enemy reinforcements are coming. Shadow has also been seen fighting the aliens alongside Sonic. A break-in at the bank has been committed by the black aliens, a Chaos Emerald was the only thing stolen and was seen in the hands of Shadow, who has also been seen following an alien gunship."

"So, he has switched sides, eh? Deploy the second squadron now! And make sure that neither the black aliens or Shadow makes it out alive."

"Sir, yes, sir!" the officer then left and the commander then spoke to himself. "No matter what you do, Shadow. I know you allegiance lies with those aliens."


	3. Chase after the Alien Gunship

**The Shadows of the Past**

_Chapter 2: Chase After the Alien Gunship_

"Damn, those aliens, They took the Emerald. I can't let them have it!" Shadow said under his breath as he chased the Black Alien Gunship along the Lethal Highway. Shadow was fast with his air shoes, but somehow the ship was even faster. Shadow tried firing his pistol at the ship to slow it down and try to destroy, but it was protected by some sort of green energy shield and his shots just bounced off.

Shadow's pistol then ran out of ammo soon after, so he just tossed it to the side of the road and continued to chase the gunship until... he fell off the highway! Ok, actually there was a section of the highway that was blasted off, Shadow didn't notice it and fell down to the lower section. Luckily his air shoes allowed him to hover a bit to help ensure a safe landing or he would fall face-first into the pavement.

Shadow then looked around and seen that the gunship was still on the upper highway. Shadow know he had to somehow get back on the upper section, but his air shoes only allow him to hover, but not fly. So Shadow ran along the lower highway, hoping he can find a way back on up. It wasn't long, though, until he ran into Sonic again.

"Shadow, let me help you bring down that ship." Sonic said as he stopped Shadow. "And why do you want to help?" Shadow asked, annoyed that Sonic was making him lose precious time. "Simple, I know this highway better that anyone else, without me, you might get lost" Sonic replied. Shadow agreed, but he would of rather liked to do this alone.

The lower highway was much like a long and twisted roller coaster, unlike the straight and smooth upper highway. There were many GUN soldiers positioned along the highway also. They fired at Shadow, but he swiftly knocked them out with his speed. "Shadow, what is it you have done? Why are the soldiers attacking us?" Sonic asked as he watched Shadow take a sub-machine gun from one of the unconscious soldiers. "I did nothing, absolutely nothing." Shadow replied, "Sonic, I appreciate your help, but I must do this, alone." Shadow pointed his gun at Sonic's head. Sonic agreed really quickly "Ok! Ok! I guess you must have your reasons then."

Leaving Sonic behind, Shadow found a path that lead back to the upper highway. He then looked around for the gunship. Shadow didn't find it until it flew right over his head. Shadow quickly fired at the ship and the shield turned from green to yellow. Shadow realized that the shield was weakening, and that he could be ably to eventually destroy it.

But chasing the ship was not easy this time, the ship dropped bombs everywhere, hoping to shake Shadow off it's tail. And if that wasn't enough, it also was firing energy shots at Shadow, but Shadow was persistent, he dodged the bombs and avoided most of the shots. He also continued to shot at the ship, and eventually the shield weakened even farther, it was now red and continued to flicker in and out.

Shadow knew a few more shots will finish the ship, but he was losing speed quickly. Once he came to a shop, he checked his shoes. The gold rings that powered his air shoes and allowed him to run fast were shattered. Shadow cursed the aliens for what they did, for now he can't catch the ship. So now Shadow walked along the destroyed highway, he looked up and seen a couple of red towers, they were originally part of the Highway, but now they were pretty much rubble.

As Shadow stared at the towers, an image came back to him from the not to distant past. Shadow remembered being here, the highway then was still brand new and the construction on it was still unfinished. He was running along the highway, destroying all of the GUN robots in his path. Then he remembered fighting Sonic here as well. As he snapped out of his flashback, Shadow wondered "What was I even doing here before? Who was I running from? And Why was I fighting Sonic?"

Shadow know he had to keep going in order to even find any answers so he continued to walk along the road. But he quickly seen an unusual weapon on the ground, it looked like a normal rifle, but it was black with several red stripes on it. Shadow quickly took a liking to this gun and tossed aside his old sub-machine gun. But Shadow didn't have long to admire the now dubbed "Shadow Rifle" until...

"FREEZE!" a voice behind Shadow said, he turned around to see who it was. The voice came from a GUN soldier on a motorcycle. (The bike was obviously a Chopper, painted black was also had the GUN logo on it as well.) "Drop the weapon and put you hands into the air" The soldier then demanded, but Shadow did or said nothing. Instead he tackled the soldier, boarded the bike, and sped off to catch the gunship.

It wasn't long until the alien gunship was within his sights. He tried to aim with his new rifle, but because of it's weight, Shadow missed his target and accidently hit a GUN robot. The force of the shot caused the mech to instantly explode. Shadow realized the immense power of this weapon and this time he had a plan. He drove is bike off a car, using it like a ramp. And then he jumped off the bike while it was still in the air. Once he was directly above the ship, he fired a couple of shots at it. The shield instantly designated and the ship exploded.

Shadow did stop the ship, but he was still high up in the air. If he did hit the ground, he would face a major injury. But he had nothing to break his fall with. Shadow was falling fast and was about to land into the gunship's remains. He braced himself for the impact, and then...

Poof! An airbag popped out of the ruins. Shadow safely landed on the airbag. He then hopped off and picked up the emerald laying amongst all the rubble. Shadow then walked away from the gunship, heading towards Central City. He then looked behind him and said out loud "What kind of idiot puts an airbag in a gunship?"


	4. Punishment of Disobeadence

Sorry for the lack of updates, I've been...busy. And I've also had a lack of ideas to progress in this. But here is the next chapter.

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**The Shadows of the Past**

_Chapter 3: Punishment of Disobedience_

Shadow walked along the street, headed for Central City. In one hand he held his Shadow Rifle, in the other, a green Chaos Emerald that was glowing with intense energy. Unknown to Shadow, the black and red star-like alien was following him. When Shadow stopped to look at the Chaos Emerald that he gotten, it felt like he couldn't move his own body anymore. Slowly, his hand with the Emerald slowly lifted into the air and his mouth spoke the words "Chaos Control" the emerald glowed even brighter then before and it engulfed him in it. Then when the light disappeared, there was only the Shadow Rifle left lying on the ground in the place where Shadow once was.

When Shadow finally regained control, he open his eyes and much to his amazement noticed that he was floating in space. The large, black, robe-wearing alien materialized in front of him. "Shadow, why did you even help those humans? You've seen that they didn't want you around." The alien said as soon as Shadow seen him. Shadow was unfazed by those words and immediately shot back at him "So, I don't care. maybe I help them because that is what I feel is right, maybe I help them because I know who the greater evil is and it's you, or maybe I help them because that are the only ones I trust have any form of clues to my past." Though how confident Shadow's statement sounded, there was still a hint of uncertainly in his voice.

"Really, is that was you really believe in? Well, I have the real truth of your past, and that truth is that the Professor created you to help me get the Chaos Emeralds. I wonder how upset he would be if he knew that you are not doing what you are supposed to do?" that alien stated "But since you did disobey me, you need to not only be punished, but also motivated to do what I order you to do. I already have one of my most elite weapons, the Black Bull, attacking Central City, and if you want to try and help the humans there, it's already too late, anything that gets in the way of Black Bull is incinerated to a crisp. Now as for you, Shadow, When I tried to get the Master Emerald for my plans, It was shattered into pieces, I feel some of the energy of the Master Emerald and a Chaos Emerald in the Glyphic Canyon, So I need you to get them for me"

Before Shadow could respond to what the alien said, There was another bright light soon, the endless space that Shadow was in was soon replaced by the sight of the tall mountains and ancient ruins of the Glyphic Canyon. Shadow proceeded to walk forward, but his body wouldn't listen to what his mind was telling him to do. Suddenly, he heard the alien's voice inside his head saying "Shadow, this is your punishment, I'll control you to do what I tell you to do until you do realize your true purpose. Now, you WILL fetch me the Chaos Emerald here and the Master Emerald piece." Under the alien's control, there were only 2 words that Shadow was allowed to speak, "Yes, Master"

Although Shadow's body was under control, his thoughts weren't. Walking through the canyon, Shadow though that the many mountains, some with a faint pumpkin-like face painted on them, looked extremely familiar. He can just barely remember running through these canyons, chasing after some sort of plane. He couldn't dwell on that for long because suddenly, his body was breaking into a run, but a somewhat slow run because the power rings that fuel his Air Shoes were shattered from before. GUN soldiers were stationed around the canyon to help fight off the aliens that were there. Shadow wanted to stop and fight the aliens, but he couldn't seem to shake off the control on his body. It wasn't long until Shadow then felt a great power surge near some bird-shaped ruins. "I guess the Emerald and the M.E. Piece have gotta be in here." Shadow thought to himself. While his possessed body proceeded to walk into the ruins.

The ruins inside were damp and pitch black. Shadow hoped that his uncontrollable body knew where it was going since hie didn't. After 2 left turns, a right turn, some stairs, 2 more right turns, and a left turn into a room, there was suddenly a flood of light from an open hole in the ceiling. In that beam of light stood a shimmering green rock that was a bit bigger then Shadow's fist. Shadow's possessed hand picked up the rock, which was definitely a Master Emerald shard. Beyond that room with the M.E. piece was a spiral staircase. After going up that, Shadow found himself outside on top of the ruins. And right there by the ruins was what looked like a shrine of some sort, not like the Master Emerald shrine on Angel Island, though, this one had what looked like a small pedestal with several stone slabs with ancient markings on them outside the pedestal. On the Pedestal stood the Red Chaos Emerald, glowing brightly in Shadow's presence.

As Shadow's body approached the Emerald, he felt a warm glow of power from within. As his hand reached even closer and closer to it, the internal glow felt even warmer and warmer. Eventually, once Shadow's hand touch the Emerald, the control that the alien over Shadow severed and Shadow was once again, free. When Shadow realized this, he quickly tried to grab the Emerald, but the emerald then disappeared in front of him, Shadow seen the Mind-controlling alien with the Chaos Emerald in hand. After seeing this, Shadow quickly used Chaos Control before the alien could have a chance to control him again.

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Yeah, this chapter doesn't seem to follow the game that well, but that's what I was aiming for in the first place. I hope I get the next chapter done a lot faster then this one. (For some odd reason I had not only a lot of busy-ness, but I also had a bad case of writer's block.)

See Ya Next Chapter!


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